The death sentences were carried out yesterday in separate hangings in Tokyo, Osaka and Nagoya.
The three men were all convicted murderers but Amnesty says two of them were "in the process of preparing to apply for retrials".
Amnesty says it fears this is the beginning of a "new wave of cold-blooded killing by the State".
Presenter: Liam Cochrane
Speaker: Roseann Rife, Amnesty International's East Asia Director
RIFE: Well, we're looking back at the record on previously when Prime Minister Abe was in office and the statements that the Minister of Justice is making and we fear that this could be the beginning of increased executions.
COCHRANE: And, I mean there was some hope that things would go in the other direction, the former government under the Democratic Party of Japan set up a panel to look into the use of capital punishment in Japan. What happened to that process?
RIFE: Actually, we really don't know what happened to that process. The panel concluded its work apparently, but we haven't seen any output. There certainly was no public debate - that was what we had called for, that was what many of the NGOs who were pushing the government to take steps towards abolition of the death penalty. We're hoping that this would actually spur it, and the government would lead some debate on the issue, but we didn't see any of that come and that is what we're still hoping that we can see take place in the coming year. But, we're concerned and these executions doesn't give us much hope.
COCHRANE: Amnesty has said that these hangings raise questions about whether executions are carried out purely for political expediency. Can you explain the political motives at play here?
RIFE: I think the issue for us is that the government continues to say that it's necessary to carry out these executions because of public opinion or the mood of the public. The issue with public opinion, of course, is that it can be easily misrepresented or manipulated. We've seen in the past that public opinion rarely supports abolition of the death penalty, until a nation does actually abolish the death penalty and then public opinion polls seem to turn in the other direction.
What we do know is that the death penalty has never proven to be a better deterrent against crime than terms of imprisonment, and the claim that the Minister of Justice made yesterday that it's necessary to maintain public order in Japan is just ludicrous.
COCHRANE: Why is it ludicrous?
RIFE: As I said, we've never seen it proven that it's, it's a deterrent against crime and certainly the Japanese police and security system is quite able to deal with crime in the country and it doesn't need to resort to this form of punishment that is a violation to the right to life in order to enforce that kind of deterrent to crime.
COCHRANE: And in fact the legal system is, is incredibly harsh on crime and Japan has a conviction rate of more than 99 per cent. In that kind of context, where basically everyone whose going before a court is found guilty and is punished. Does that make it even more pressing to look carefully at those punishments?
RIFE: Absolutely. We've heard them calling for an end to the daiyo-kangoku system which is essentially a system that allows the police to hold people in stations for up to 23 days without effective access to legal counsel and we've seen that this is often a time when they obtain confessions and it's often done through torture and other forms of ill-treatment, including intimidation and sleep depravation. If you have a system that relies on this kind of confession, then you are setting yourselves up for essentially executing the people who have confessed through this system.
COCHRANE: How many more people are on death row in Japan?
RIFE: Currently we understand 134 people remain on death row and that is one of the highest numbers of individuals on death row in the last decade in Japan. So there's a real concern that we could face executions and they could be imminent and we're calling on the government to, at the very least, stop executions, put a moratorium on executions until they can actually have an effective public discussion, that we've all been calling for.